Paradigm shift in xylose isomerase usage: a novel scenario with distinct applications

Miyamoto, Renan Yuji; Melo, Ricardo Rodrigues de; Sampaio, Isabelle Lobo de Mesquita; Sousa, Amanda Silva de; Morais, Edvaldo Rodrigo de; Sargo, Cíntia Regina; Zanphorlin, L.M.

doi:10.1080/07388551.2021.1962241

Cited by 11 publications

(8 citation statements)

References 152 publications

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“…Xylose isomerase has widely been used in the production of high-fructose corn syrup (HFCS) and bioethanol [47]. It is potentially explored to produce some value-added chemicals in the food, cosmetics, and pharmaceutical industries [44]. Carboxylesterases (CEs) have been applied in xenobiotic and endobiotic degradations, biocatalysis, and drug metabolism [68].…”

Section: Discussionmentioning

confidence: 99%

Biotechnologically potential genes in a polysaccharide-degrading epibiont of the Indonesian brown algae Hydroclathrus sp.

Ethica

Zilda²,

Oedjijono

et al. 2023

Journal of Genetic Engineering and Biotechnology

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Background Marine bacteria have recently attracted increasing attention to be harnessed for the production of valuable enzymes, vitamins, and bioactive compounds. Bacteria associated with the surfaces of marine macroalgae, called epibionts, are particularly interesting from ecological and biotechnological points of view, as they often exhibit antimicrobial activities to compete with pathogenic bacteria for nutrients and spaces. In search for biotechnologically potential genes from marine bacteria, we sequenced and analysed the genome of the epibiont HI03-3b, a polysaccharide-degrading bacterium associated with the surface of the Indonesian brown algae Hydroclathrus sp. Results The algal epibiont HI03-3b has a genome of approximately 4,860,704 bp in size with 42.02 mol% G + C content, consisting of 5655 open reading frames (ORFs), 4409 genes coding for proteins (CDSs), 94 genes for tRNAs, and 32 genes for rRNAs. The genome sequence of HI03-3b was most closely related to that of Cytobacillus firmus NCTC10335 with the average amino acid identity (AAI) of 95.0 %, average nucleotide identity (ANI) of 94.1 %, and a recommended DNA-DNA hybridization (DDH) of 57.60 %. These scores are lower than the most frequently used standard for species demarcation (95% ANI cutoff) and the new species threshold (DDH > 70.0% for the same bacterial species). Some differences in genome features and gene composition were observed between HI03-3b and NCTC10335, such as genes encoding carbohydrate active enzymes. These suggest that HI03-3b is unique and likely a novel species within Cytobacillus genus, and we therefore proposed its name as Cytobacillus wakatobiense HI03-3b. Genome sequence analyses indicated the presence of genes involved not only in polysaccharide and protein degradation but also in vitamin and secondary metabolite biosynthesis. Some of them encode enzymes and compounds with biotechnological interest, such as protease, chitinase, subtilisin, pullulanase, and bacillolysin, which are often associated with antimicrobial or antibiofilm activities. This antimicrobial potential is supported by our finding that the extracellular protein fraction of this epibiont inhibited the growth of the bacterial pathogen Staphylococcus aureus. Conclusion The epibiont Cytobacillus HI03-3b harbours genes for polysaccharide and protein degradation as well as for natural product biosynthesis, suggesting its potential ecological roles in outcompeting other bacteria during biofilm formation as well as in protecting its algal host from predation. Due to the presence of genes for vitamin biosynthesis, it might also provide the algal host with vitamins for growth and development. Some of these metabolic genes are biotechnologically important, as they could become a platform for bioengineering to generate various seaweed-derived substances sustainably, such as antibiofilm agents and vitamins, which are beneficial for human health.

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Section: Discussionmentioning

confidence: 99%

Biotechnologically potential genes in a polysaccharide-degrading epibiont of the Indonesian brown algae Hydroclathrus sp.

Ethica

Zilda²,

Oedjijono

et al. 2023

Journal of Genetic Engineering and Biotechnology

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“…Nevertheless, rare reported enzymatic cascades integrating isomerase and oxidoreductase to convert xylose and redox–redox enzymatic cascades to convert xylose resulted in unsatisfactory yields 23 . Moreover, the commonly used isomerase d ‐xylose isomerase has a wide substrate scope and can also isomerize glucose and other biomass monosaccharides, making the products complicated when practical lignocellulosic substrates are harnessed 24 …”

Section: Introductionmentioning

confidence: 99%

“…23 Moreover, the commonly used isomerase D-xylose isomerase has a wide substrate scope and can also isomerize glucose and other biomass monosaccharides, making the products complicated when practical lignocellulosic substrates are harnessed. 24 A ribose-5-phosphate isomerase B from Ochrobactrum sp. (OsRpiB) was identified with unique substrate scope and can selectively convert xylose from mixtures of glucose and other biomass monosaccharides.…”

Section: Introductionmentioning

confidence: 99%

Development of an enzymatic cascade to systematically utilize lignocellulosic monosaccharide

Tang

Chen

Yu³

et al. 2022

J Sci Food Agric

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BACKGROUND The fermentation valorization of two main lignocellulosic monosaccharides, glucose and xylose, is extensively developed; however, it is restricted by limited yield and process complexity. An in vitro enzymatic cascade reaction can be an alternative approach. RESULTS In this study, a three‐stage, five‐enzyme cascade was developed to convert pretreated biomass to valuable chemicals. First, a ribose‐5‐phosphate isomerase B mutant isomerized xylose to d‐xylulose with high substrate specificity, and a d‐arabinose dehydrogenase continued to reduce d‐xylulose to d‐arabitol. Simultaneously, glucose was utilized for the coenzyme regeneration catalyzed by a glucose dehydrogenase, generating useful gluconic acid and achieving 73% of total conversion rate after 36 h. Then, six kinds of pretreated biomass lignocellulose were hydrolyzed by cellulase and hemicellulase, and corn cob was identified as the initial substrate for providing the highest monosaccharide content. A 65% conversion rate of the lignocellulosic xylose was obtained after 24 h. CONCLUSIONS This study presents a proof of concept to convert main lignocellulosic monosaccharides systematically by an enzymatic cascade at stoichiometric ratio. © 2022 Society of Chemical Industry.

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“…13 Another alternative for xylose conversion is the addition of enzymes to the culture media, such as xylose isomerase (XI), which performs the isomerization of xylose into xylulose that can be assimilated by many microorganisms, including S. cerevisiae, in a process called simultaneous isomerization and fermentation (SIF). 9,14 However, this strategy presents several bottlenecks, such as the difference between the optimal conditions for the enzyme and the microorganism besides the loss of enzymatic activity. 14 Enzymes are also expensive and can contribute to increasing the costs of the process.…”

mentioning

confidence: 99%

“…9,14 However, this strategy presents several bottlenecks, such as the difference between the optimal conditions for the enzyme and the microorganism besides the loss of enzymatic activity. 14 Enzymes are also expensive and can contribute to increasing the costs of the process. 15 The use of natural pentose-fermenting strains is an alternative for the co-consumption of hexoses and pentoses because it does not require additional enzymes supplemented to the media 2,16 but these strains usually present specific demands for their cultivation, like media supplementation and controlled aeration.…”

mentioning

confidence: 99%

Screening of yeast co‐culture using crude hydrolysate for co‐fermentation of pentose and hexose

Sandri

Milessi

Zangirolami

et al. 2023

Biofuels Bioprod Bioref

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The use of all sugars from biomass fractionation – that is, hexoses and pentoses – is essential to develop feasible processes in a biorefinery context. Hexoses are converted into different products by most microorganisms. The main issue is the conversion of pentoses, especially when mixed with hexoses. Improving sugar conversion in co‐fermentation is a major challenge, which was explored in this work. Co‐culture using Saccharomyces cerevisiae and evolved Kluyveromyces marxianus strains was evaluated by screening using 24 deep‐well plates. Glucose depletion and 83% of xylose conversion were achieved with supplemented hemicellulosic hydrolysate medium (medium volume corresponding to 2/5 of deep‐well volume), and initial cell concentrations of 2.5 g L‐1 for each yeast, incubated at 150 rpm. The screening strategy provided reliable data that confirmed the co‐culture as a promising approach for the co‐assimilation of biomass‐derived sugars. The importance of aeration control for effective xylose assimilation was also pointed out.

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Paradigm shift in xylose isomerase usage: a novel scenario with distinct applications

Cited by 11 publications

References 152 publications

Biotechnologically potential genes in a polysaccharide-degrading epibiont of the Indonesian brown algae Hydroclathrus sp.

Biotechnologically potential genes in a polysaccharide-degrading epibiont of the Indonesian brown algae Hydroclathrus sp.

Development of an enzymatic cascade to systematically utilize lignocellulosic monosaccharide

Screening of yeast co‐culture using crude hydrolysate for co‐fermentation of pentose and hexose

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